Estimating Population-Level Coancestry Coefficients by an Admixture F Model |
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Authors: | Markku Karhunen Otso Ovaskainen |
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Institution: | Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland |
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Abstract: | In this article, we develop an admixture F model (AFM) for the estimation of population-level coancestry coefficients from neutral molecular markers. In contrast to the previously published F model, the AFM enables disentangling small population size and lack of migration as causes of genetic differentiation behind a given level of FST. We develop a Bayesian estimation scheme for fitting the AFM to multiallelic data acquired from a number of local populations. We demonstrate the performance of the AFM, using simulated data sets and real data on ninespine sticklebacks (Pungitius pungitius) and common shrews (Sorex araneus). The results show that the parameterization of the AFM conveys more information about the evolutionary history than a simple summary parameter such as FST. The methods are implemented in the R package RAFM. |
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Keywords: | coancestry identity by descent (IBD) FST admixture F model (AFM) Bayesian inference |
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